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Modelling structural properties of cyanine dye nanotubes at coarse-grained level

Self-assembly is a ubiquitous process spanning from biomolecular aggregates to nanomaterials. Even though the resulting aggregates can be studied through experimental techniques, the dynamic pathways of the process and the molecular details of the final structures are not necessarily easy to resolve...

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Detalles Bibliográficos
Autores principales: Patmanidis, Ilias, Souza, Paulo C. T., Sami, Selim, Havenith, Remco W. A., de Vries, Alex H., Marrink, Siewert J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: RSC 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9419059/
https://www.ncbi.nlm.nih.gov/pubmed/36133510
http://dx.doi.org/10.1039/d2na00158f
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author Patmanidis, Ilias
Souza, Paulo C. T.
Sami, Selim
Havenith, Remco W. A.
de Vries, Alex H.
Marrink, Siewert J.
author_facet Patmanidis, Ilias
Souza, Paulo C. T.
Sami, Selim
Havenith, Remco W. A.
de Vries, Alex H.
Marrink, Siewert J.
author_sort Patmanidis, Ilias
collection PubMed
description Self-assembly is a ubiquitous process spanning from biomolecular aggregates to nanomaterials. Even though the resulting aggregates can be studied through experimental techniques, the dynamic pathways of the process and the molecular details of the final structures are not necessarily easy to resolve. Consequently, rational design of self-assembling aggregates and their properties remains extremely challenging. At the same time, modelling the self-assembly with computational methods is not trivial, because its spatio-temporal scales are usually beyond the limits of all-atom based simulations. The use of coarse-grained (CG) models can alleviate this limitation, but usually suffers from the lack of optimised parameters for the molecular constituents. In this work, we describe the procedure of parametrizing a CG Martini model for a cyanine dye (C8S3) that self-assembles into hollow double-walled nanotubes. First, we optimised the model based on quantum mechanics calculations and all-atom reference simulations, in combination with available experimental data. Then, we conducted random self-assembly simulations, and the performance of our model was tested on preformed assemblies. Our simulations provide information on the time-dependent local arrangement of this cyanine dye, when aggregates are being formed. Furthermore, we provide guidelines for designing and optimising parameters for similar self-assembling nanomaterials.
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spelling pubmed-94190592022-09-20 Modelling structural properties of cyanine dye nanotubes at coarse-grained level Patmanidis, Ilias Souza, Paulo C. T. Sami, Selim Havenith, Remco W. A. de Vries, Alex H. Marrink, Siewert J. Nanoscale Adv Chemistry Self-assembly is a ubiquitous process spanning from biomolecular aggregates to nanomaterials. Even though the resulting aggregates can be studied through experimental techniques, the dynamic pathways of the process and the molecular details of the final structures are not necessarily easy to resolve. Consequently, rational design of self-assembling aggregates and their properties remains extremely challenging. At the same time, modelling the self-assembly with computational methods is not trivial, because its spatio-temporal scales are usually beyond the limits of all-atom based simulations. The use of coarse-grained (CG) models can alleviate this limitation, but usually suffers from the lack of optimised parameters for the molecular constituents. In this work, we describe the procedure of parametrizing a CG Martini model for a cyanine dye (C8S3) that self-assembles into hollow double-walled nanotubes. First, we optimised the model based on quantum mechanics calculations and all-atom reference simulations, in combination with available experimental data. Then, we conducted random self-assembly simulations, and the performance of our model was tested on preformed assemblies. Our simulations provide information on the time-dependent local arrangement of this cyanine dye, when aggregates are being formed. Furthermore, we provide guidelines for designing and optimising parameters for similar self-assembling nanomaterials. RSC 2022-06-20 /pmc/articles/PMC9419059/ /pubmed/36133510 http://dx.doi.org/10.1039/d2na00158f Text en This journal is © The Royal Society of Chemistry https://creativecommons.org/licenses/by/3.0/
spellingShingle Chemistry
Patmanidis, Ilias
Souza, Paulo C. T.
Sami, Selim
Havenith, Remco W. A.
de Vries, Alex H.
Marrink, Siewert J.
Modelling structural properties of cyanine dye nanotubes at coarse-grained level
title Modelling structural properties of cyanine dye nanotubes at coarse-grained level
title_full Modelling structural properties of cyanine dye nanotubes at coarse-grained level
title_fullStr Modelling structural properties of cyanine dye nanotubes at coarse-grained level
title_full_unstemmed Modelling structural properties of cyanine dye nanotubes at coarse-grained level
title_short Modelling structural properties of cyanine dye nanotubes at coarse-grained level
title_sort modelling structural properties of cyanine dye nanotubes at coarse-grained level
topic Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9419059/
https://www.ncbi.nlm.nih.gov/pubmed/36133510
http://dx.doi.org/10.1039/d2na00158f
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